galaxy-automation
CommunityAutomate Galaxy workflows with BioBlend & Planemo.
System Documentation
What problem does it solve?
This Skill provides expert tooling and knowledge to automate Galaxy workflows using BioBlend (Galaxy API) and Planemo, enabling programmatic workflow invocation, dataset management, and status tracking.
Core Features & Use Cases
- API-driven workflow invocation: Launch Galaxy workflows and monitor their progress from a script or CI.
- Batch processing: Run multiple workflow invocations across histories and datasets in parallel with controlled concurrency.
- Error handling & retries: Detect failed invocations and automatically retry with configurable parameters.
- Use Case: Automate the processing of dozens of sample datasets by invoking a single workflow across all inputs and collecting results in a report.
Quick Start
Install dependencies with pip: pip install bioblend planemo. Then create a Galaxy connection using GalaxyInstance(url="https://usegalaxy.org", key="YOUR_API_KEY") and run a simple workflow invocation via the API or Planemo. Replace URL and key with your credentials.
You can expand this setup to batch process multiple histories, datasets, and workflows.
Dependency Matrix
Required Modules
Components
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: galaxy-automation Download link: https://github.com/Delphine-L/claude_global/archive/main.zip#galaxy-automation Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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